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1Clear out junk files and repair common Windows errors2Scan for outdated or missing drivers - takes under a minute3Repair Windows errors before they cause bigger problemsThe “methane-oxidising enzyme” depends on how methane is being consumed. In oxygen-free environments, anaerobic methanotrophic archaea use methyl-coenzyme M reductase (MCR); aerobic methanotrophic bacteria use methane monooxygenase (MMO) to convert methane into methanol. A 2025 study provided atomic-resolution structures of MCR from anaerobic methane-oxidising archaea and revealed extensive chemical modifications, including a previously unreported one. It sharpened the picture of the enzyme, but did not settle every detail of how methane oxidation works.
Which enzyme oxidises methane?
There is no single answer without specifying the conditions. Two distinct enzyme systems are relevant:
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| Context | Enzyme | What it does |
|---|---|---|
| Anaerobic methane oxidation | Methyl-coenzyme M reductase (MCR) | Used by anaerobic methanotrophic archaea (ANME) to oxidise methane without oxygen. |
| Aerobic methane oxidation | Methane monooxygenase (MMO) | Uses oxygen to convert methane to methanol in methanotrophic bacteria. |
These are not two names for the same enzyme. MCR is also central to biological methane production: related MCR enzymes can run in reverse in methanotrophs. MMO belongs to the separate oxygen-dependent pathway.
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Müller and colleagues reported atomic-resolution structures of MCR from microbial enrichments containing freshwater nitrate-reducing ANME-2d and marine ANME-2c living with bacterial partners. The work examined three enzymes and reported seven post-translational modifications across them. One finding was a novel 3(S)-methylhistidine modification on the γ-chain of both ANME-2d MCRs. The study, published in Nature Communications on September 5, 2025, adds structural detail to an enzyme that is difficult to investigate because ANME have not been isolated in culture; the researchers used microbial enrichments instead.
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What the structures say about the reaction
The researchers used krypton labelling and did not detect internal channels that would facilitate alkane diffusion to the active site. The paper argues that methane-oxidising MCR should follow the same radical reaction mechanism proposed for methane-generating MCR homologues. That is an inference from the structural results and similarities between enzymes—not experimental resolution of every step in the ANME reaction.
The distinction matters: a high-resolution structure can show the enzyme’s architecture and chemical modifications, but it does not by itself establish the full sequence of events during catalysis.
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A separate 2025 discovery: how methane-producing MCR is activated
A different 2025 study investigated how MCR is activated in methane-producing organisms. Its focus was an ATP-dependent activation complex, not the atomic-resolution structures of methane-oxidising ANME enzymes. The active-site cofactor F430 contains nickel, and its Ni(I) state is necessary for catalysis. The study identified a role for the small protein McrC and other methanogenic marker proteins in the activation process.
The associated account from TU Berlin, dated April 17, 2025, describes three specialised iron-sulfur metal complexes involved in activation and presents a possible evolutionary link to nitrogenase. This helps explain how methane-producing MCR is made catalytically ready; it should not be confused with the ANME structural study. Its relevance to methane oxidation is that MCR homologues in methanotrophs operate in reverse, as noted in the Nature paper on the activation complex.
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How the aerobic MMO pathway differs
In aerobic methanotrophs, MMO catalyses the conversion of methane to methanol. A 2015 Nature study of soluble MMO examined compound Q, an intermediate containing a two-iron Fe(IV) cluster that reacts with methane and inserts one oxygen atom. In that reaction context, the paper gives the methane C–H bond strength as 105 kcal mol−1.
The same paper cited an estimate of approximately one billion tons of methane prevented from entering the atmosphere each year in connection with methane monooxygenase. That is the paper’s published contextual estimate, not a newly verified measurement of present-day global flux. A separate 2026 paper reports that copper acquisition from minerals promotes aerobic methane oxidation, but it concerns this aerobic context rather than the 2025 ANME MCR structures: Communications Earth & Environment, March 18, 2026.
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What is solved—and what remains open
- Resolved: Atomic-resolution structures are now reported for three MCR enzymes from ANME enrichments, with seven post-translational modifications identified and a novel γ-chain modification found in both studied ANME-2d enzymes.
- Supported, not fully demonstrated: The ANME enzymes are expected to use the radical mechanism proposed for methane-generating MCR homologues, based on structural evidence.
- Not the same result: The ATP-driven activation complex study concerns methane-producing MCR; it is distinct from the ANME structures.
- A separate pathway: MMO oxidises methane to methanol in aerobic bacteria, using oxygen; it is not MCR.
So the “mystery” is narrower than the headline suggests. The 2025 structural work substantially clarified the architecture and modifications of anaerobic methane-oxidising MCR, while the precise catalytic mechanism remains a question of evidence beyond structure alone.
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